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PLoS Computational Biology, Volume 20
Volume 20, Number 1, January 2024
- Marcus Kaiser
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Ten simple rules for establishing an experimental lab. - Gabriel Reuben Smith
Ten simple rules for using large language models in science, version 1.0.
- Alice Bruel
The spinal cord facilitates cerebellar upper limb motor learning and control; inputs from neuromusculoskeletal simulation. - Enrique R. Sebastian, Julio Esparza
Quantifying the distribution of feature values over data represented in arbitrary dimensional spaces. - Aakash Pandey
Wildlife vaccination strategies for eliminating bovine tuberculosis in white-tailed deer populations. - Yoav Ger
Harnessing the flexibility of neural networks to predict dynamic theoretical parameters underlying human choice behavior. - Jinchao Lv, Jin Wang
Landscape quantifies the intermediate state and transition dynamics in ecological networks. - Yong-Jin Huang
Detecting shifts in nonlinear dynamics using Empirical Dynamic Modeling with Nested-Library Analysis. - Jiarui Feng, S. Peter Goedegebuure, Amanda Zeng, Ye Bi, Ting Wang, Philip R. O. Payne, Li Ding, David DeNardo, William Hawkins, Ryan C. Fields, Fuhai Li
sc2MeNetDrug: A computational tool to uncover inter-cell signaling targets and identify relevant drugs based on single cell RNA-seq data. - Elizabeth Lawson-Keister, Tao Zhang, Fatemeh Nazari, François Fagotto
Differences in boundary behavior in the 3D vertex and Voronoi models. - Lucas Castillo
Explaining the flaws in human random generation as local sampling with momentum. - Haiqing Zhao
The role of cryptic ancestral symmetry in histone folding mechanisms across Eukarya and Archaea. - Florian G. Pflug
Genome replication in asynchronously growing microbial populations. - Paul F. Lang
Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells. - Chin-Hsuan Sophie Lin
Are we really Bayesian? Probabilistic inference shows sub-optimal knowledge transfer. - Tijl Grootswagers
Mapping the dynamics of visual feature coding: Insights into perception and integration. - Michael J. Plank
Near-term forecasting of Covid-19 cases and hospitalisations in Aotearoa New Zealand. - Avik Mukherjee
Plasticity of growth laws tunes resource allocation strategies in bacteria. - Sjoerd Terpstra
Adaptive foraging of pollinators fosters gradual tipping under resource competition and rapid environmental change. - Christopher A. Mancuso
Joint representation of molecular networks from multiple species improves gene classification. - Eric Elmoznino
High-performing neural network models of visual cortex benefit from high latent dimensionality. - Jian Zou
Systems approach for congruence and selection of cancer models towards precision medicine. - Eduardo Jardón-Valadez
Tracking conformational transitions of the gonadotropin hormone receptors in a bilayer of (SDPC) poly-unsaturated lipids from all-atom molecular dynamics simulations. - H. Robert Frost
Tissue-adjusted pathway analysis of cancer (TPAC): A novel approach for quantifying tumor-specific gene set dysregulation relative to normal tissue. - Tyler S. Manning
Transformations of sensory information in the brain suggest changing criteria for optimality. - Karan Kabbur Hanumanthappa Manjunatha
Controlling target brain regions by optimal selection of input nodes. - Kaiser J. Loell, Ryan Z. Friedman
Transcription factor interactions explain the context-dependent activity of CRX binding sites. - Hong An
Gene expression bias between the subgenomes of allopolyploid hybrids is an emergent property of the kinetics of expression. - Janne J. Luppi
Virtual neural network-guided optimization of non-invasive brain stimulation in Alzheimer's disease. - Maki Sudo
Diffusive mediator feedbacks control the health-to-disease transition of skin inflammation. - Giovanni Lo Iacono, Alasdair J. C. Cook, Gianne Derks, Lora E. Fleming, Nigel French, Emma L. Gillingham, Laura C. Gonzalez Villeta, Clare Heaviside, Roberto La Ragione, Giovanni Leonardi, Christophe E. Sarran, Sotiris Vardoulakis, Francis Senyah, Arnoud H. M. van Vliet, Gordon Nichols:
A mathematical, classical stratification modeling approach to disentangling the impact of weather on infectious diseases: A case study using spatio-temporally disaggregated Campylobacter surveillance data for England and Wales. - Martin Grunnill
Modelling disease mitigation at mass gatherings: A case study of COVID-19 at the 2022 FIFA World Cup. - Shunsuke Koseki
Identifying essential factors for energy-efficient walking control across a wide range of velocities in reflex-based musculoskeletal systems. - Virginia Dominguez-Garcia
The structure and robustness of ecological networks with two interaction types. - Sebastian Idesis
Functional hierarchies in brain dynamics characterized by signal reversibility in ferret cortex. - Laura Schmid
Postinhibitory excitation in motoneurons can be facilitated by hyperpolarization-activated inward currents: A simulation study. - Anand Ramachandran
PandoGen: Generating complete instances of future SARS-CoV-2 sequences using Deep Learning. - Chen Beer
Revealing and reshaping attractor dynamics in large networks of cortical neurons. - Sizhe Qiu
Inferred regulons are consistent with regulator binding sequences in E. coli. - Pablo Alvarez
Predicting primate tongue morphology based on geometrical skull matching. A first step towards an application on fossil hominins. - Marine Louarn, Guillaume Collet, Ève Barré, Thierry Fest, Olivier Dameron
Regulus infers signed regulatory relations from few samples' information using discretization and likelihood constraints. - Javier Robles
Integrated meta-analysis of colorectal cancer public proteomic datasets for biomarker discovery and validation. - Bryan Shin
Examining B-cell dynamics and responsiveness in different inflammatory milieus using an agent-based model. - Leo Zeitler
A genome-wide comprehensive analysis of nucleosome positioning in yeast. - Pascal P. Klamser
Inferring country-specific import risk of diseases from the world air transportation network. - Andrea Papale
Chromatin phase separated nanoregions explored by polymer cross-linker models and reconstructed from single particle trajectories. - Kieran D. Lamb
Mutational signature dynamics indicate SARS-CoV-2's evolutionary capacity is driven by host antiviral molecules. - Ian T. Ellwood
Short-term Hebbian learning can implement transformer-like attention. - Raymond Copeland, Christopher Zhang
Spatial constraints and stochastic seeding subvert microbial arms race. - Michiel van Boven
Estimation of introduction and transmission rates of SARS-CoV-2 in a prospective household study. - David L. Krongauz
Vision-based collective motion: A locust-inspired reductionist model. - Mehran Fazli
Conversion of spikers to bursters in pituitary cell networks: Is it better to disperse for maximum exposure or circle the wagons? - Beatriz Ocaña-Tienda
Radiation necrosis after radiation therapy treatment of brain metastases: A computational approach. - Ata Kalirad
Spatial and temporal heterogeneity alter the cost of plasticity in Pristionchus pacificus. - Magdalena Kozielska
A neural network model for the evolution of learning in changing environments. - Yaojia Chen
AutoEdge-CCP: A novel approach for predicting cancer-associated circRNAs and drugs based on automated edge embedding. - Louis Yat Hin Chan
Modeling geographic vaccination strategies for COVID-19 in Norway.
- Paul J. N. Brodersen
Somnotate: A probabilistic sleep stage classifier for studying vigilance state transitions. - Rituparna Samanta
Implicit model to capture electrostatic features of membrane environment. - Said el Bouhaddani
Statistical integration of multi-omics and drug screening data from cell lines.
- Sebastian Himbert
MEDUSA: A cloud-based tool for the analysis of X-ray diffuse scattering to obtain the bending modulus from oriented membrane stacks. - Hua-Chang Chen, Jing Wang
FindAdapt: A python package for fast and accurate adapter detection in small RNA sequencing.
Volume 20, Number 2, February 2024
- Joachim Goedhart
Studentsourcing - Aggregating and reusing data from a practical cell biology course.
- Helena Klara Jambor
Ten simple rules for designing graphical abstracts.
- Martijn A. de Jong
The shapes of elongating gastruloids are consistent with convergent extension driven by a combination of active cell crawling and differential adhesion. - Kameel Khabaz
The geometric evolution of aortic dissections: Predicting surgical success using fluctuations in integrated Gaussian curvature. - Jacob B. Roberts
Foldy: An open-source web application for interactive protein structure analysis. - Sarah Percival, Joyce G. Onyenedum, Daniel H. Chitwood, Aman Y. Husbands
Topological data analysis reveals core heteroblastic and ontogenetic programs embedded in leaves of grapevine (Vitaceae) and maracuyá (Passifloraceae). - Matthijs Pals
Trained recurrent neural networks develop phase-locked limit cycles in a working memory task. - Jane Knöchel
Index analysis: An approach to understand signal transduction with application to the EGFR signalling pathway. - Etienne Thoret
Sleep deprivation detected by voice analysis. - Sarvenaz Sarabipour
Trafficking dynamics of VEGFR1, VEGFR2, and NRP1 in human endothelial cells. - Connor R. King
Stochastic model of vesicular stomatitis virus replication reveals mutational effects on virion production. - Te Liu
Reconciling ASPP-p53 binding mode discrepancies through an ensemble binding framework that bridges crystallography and NMR data. - Yu Feng
Attractor neural networks with double well synapses. - Keith E. Kennedy
Multiscale networks in multiple sclerosis. - Zhijie Feng, Robert Marsland III, Jason W. Rocks, Pankaj Mehta
Emergent competition shapes top-down versus bottom-up control in multi-trophic ecosystems. - Joe Hilton
A beta-Poisson model for infectious disease transmission. - Josepha Godivier
Compressive stress gradients direct mechanoregulation of anisotropic growth in the zebrafish jaw joint. - Linxing Preston Jiang
Dynamic predictive coding: A model of hierarchical sequence learning and prediction in the neocortex. - Xiang Liu
An Epigenomic fingerprint of human cancers by landscape interrogation of super enhancers at the constituent level. - Meenal Datta
Mathematical model of oxygen, nutrient, and drug transport in tuberculosis granulomas. - Samuel H. A. von der Dunk
Intracellular signaling in proto-eukaryotes evolves to alleviate regulatory conflicts of endosymbiosis. - Nathan LaPierre
Accounting for isoform expression increases power to identify genetic regulation of gene expression. - Kemin Zhu, Ling Yin
Generating synthetic population for simulating the spatiotemporal dynamics of epidemics. - Carlos S. N. Brito, Wulfram Gerstner
Learning what matters: Synaptic plasticity with invariance to second-order input correlations. - Zhenxing Guo, Daoyu Duan, Wen Tang
magpie: A power evaluation method for differential RNA methylation analysis in N6-methyladenosine sequencing. - Lachlan Baer
Differential allelic representation (DAR) identifies candidate eQTLs and improves transcriptome analysis. - Jiao Zhao, Ke Chen, Bernhard O. Palsson
StressME: Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses. - Li-Dunn Chen
Enhancing predictive performance for spectroscopic studies in wildlife science through a multi-model approach: A case study for species classification of live amphibians. - Jakub Köry
Enhanced perfusion following exposure to radiotherapy: A theoretical investigation. - András Zeke, Toby J. Gibson, Laszlo Dobson
Linear motifs regulating protein secretion, sorting and autophagy in Leishmania parasites are diverged with respect to their host equivalents. - Martin L. L. R. Barry
Fast adaptation to rule switching using neuronal surprise. - Sven Wientjes
The successor representation subserves hierarchical abstraction for goal-directed behavior. - Alexander D. Bird
Robust and consistent measures of pattern separation based on information theory and demonstrated in the dentate gyrus. - Jose Gabriel Nino Barreat
Ecological and evolutionary dynamics of cell-virus-virophage systems. - Natalie Schieferstein
Intra-ripple frequency accommodation in an inhibitory network model for hippocampal ripple oscillations. - Francesco Pinotti
EPINEST, an agent-based model to simulate epidemic dynamics in large-scale poultry production and distribution networks. - Quintessa Hay
Age-dependent ventilator-induced lung injury: Mathematical modeling, experimental data, and statistical analysis. - Juliette Cooke
Genome scale metabolic network modelling for metabolic profile predictions. - Eshan S. King
Diverse mutant selection windows shape spatial heterogeneity in evolving populations. - Tom Van Wouwe
A simulation framework to determine optimal strength training and musculoskeletal geometry for sprinting and distance running. - Tomas Barta
Shared input and recurrency in neural networks for metabolically efficient information transmission. - Moritz Groden
A biologically inspired repair mechanism for neuronal reconstructions with a focus on human dendrites. - Nicholas Tolley
Methods and considerations for estimating parameters in biophysically detailed neural models with simulation based inference. - Paul Soulos, Leyla Isik
Disentangled deep generative models reveal coding principles of the human face processing network. - Pan Li, Jae Kyoung Kim
Circadian regulation of sinoatrial nodal cell pacemaking function: Dissecting the roles of autonomic control, body temperature, and local circadian rhythmicity. - Sangjeong Lee, Hyunwoo Kim
Bidirectional de novo peptide sequencing using a transformer model. - R. Dustin Schaeffer
ECOD domain classification of 48 whole proteomes from AlphaFold Structure Database using DPAM2. - Chen Zhang
STGIC: A graph and image convolution-based method for spatial transcriptomic clustering. - Rui Wang, Zhilin Qu
Dissecting the roles of calcium cycling and its coupling with voltage in the genesis of early afterdepolarizations in cardiac myocyte models. - Takahiro Kohsokabe
Developmental hourglass: Verification by numerical evolution and elucidation by dynamical-systems theory. - Denise Vlachou, Maria Veretennikova, Laura Usselmann, Vadim Vasilyev, Sascha Ott, Georg A. Bjarnason, Robert Dallmann
TimeTeller: A tool to probe the circadian clock as a multigene dynamical system. - Bonnie V. Dougherty, Connor J. Moore, Kristopher D. Rawls
Identifying metabolic adaptations characteristic of cardiotoxicity using paired transcriptomics and metabolomics data integrated with a computational model of heart metabolism. - Bastiaan J. R. Cockx
Is it selfish to be filamentous in biofilms? Individual-based modeling links microbial growth strategies with morphology using the new and modular iDynoMiCS 2.0. - Margaritis Voliotis
HormoneBayes: A novel Bayesian framework for the analysis of pulsatile hormone dynamics.
- Daniele Dall'Olio
Covering Hierarchical Dirichlet Mixture Models on binary data to enhance genomic stratifications in onco-hematology. - Yongtao Ye, Marcus H. Shum, Joseph L. Tsui, Guangchuang Yu
Robust expansion of phylogeny for fast-growing genome sequence data. - Aaron L. Phillips
CLAW: An automated Snakemake workflow for the assembly of chloroplast genomes from long-read data. - Luca Sesta
Inference of annealed protein fitness landscapes with AnnealDCA. - Alexander Borst
Connectivity Matrix Seriation via Relaxation. - Dennis Eschweiler
Denoising diffusion probabilistic models for generation of realistic fully-annotated microscopy image datasets. - Lily Monnier
A novel batch-effect correction method for scRNA-seq data based on Adversarial Information Factorization. - Martin H. P. Fernholz, Drago A. Guggiana Nilo, Tobias Bonhoeffer, Andreas M. Kist
DeepD3, an open framework for automated quantification of dendritic spines.
- Tyson L. Swetnam
CyVerse: Cyberinfrastructure for open science. - Hong Seo Lim
Quantifying the clusterness and trajectoriness of single-cell RNA-seq data.
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